This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Keep Format and Individual fields after annotating VCF with VEP

Hi, I got stuck, my intention was to use VEP on my VCF and later do a VariantsToTable, but annotations of VEP are added to a field into INFO called CSQ and I can not figure out how to get them as VariantsToTable does with INFO column. Any idea how to extract it using VariantsToTable from GATK or better suggestion?

Thanks in advance!

CLOSE RELATED TO:Keep Format and Individual fields when annotating VCF with VEP

vep vcf annotation info csq
• 2,532 views • link
written by MasMarius • MasMarius

What are you trying to do with the data overall? Why is the data being in the CSQ field a problem?

• 1 views • link
written by Emily Emily

Hi Emily, It is not a problem, just want to switch it into a more readable for EXCEL/CALC. Converting CSQ (info) to a column with each vep annotation following a order such as CHROM,QUAL,Feature,Biotype,GNOMAD,Consequence.. and i will like to know if, does exists any tool for it?

• 1 views • link
written by MasMarius • MasMarius

0 answers

No answers yet.

Log in to answer this question.

More posts like this